I had a problem with my middle mouse key before that was caused by an external program (called 7plus, which is made using autohotkey). The cause of your problem could be some other program, possibly something scripted in autohotkey.
not that i know. Its just a collection of scripts - not something that modifies any existing max files. Does the alt key with the viewport navigation work? Or the shift key when duplicating objects or the global F1 key for the help files?